Variant 11-66756337-CT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2

The ENST00000525449.6(C11orf80):c.-149-6del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0152 in 1,081,708 control chromosomes in the GnomAD database, including 84 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.011 ( 12 hom., cov: 31)

Exomes 𝑓: 0.016 ( 72 hom. )

Consequence

C11orf80
ENST00000525449.6 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.538

Variant links:

Genes affected

C11orf80 (HGNC:26197): (TOP6B like initiator of meiotic double strand breaks) Predicted to be involved in meiotic DNA double-strand break formation and reciprocal meiotic recombination. Predicted to be located in chromosome. Implicated in gestational trophoblastic neoplasm. [provided by Alliance of Genome Resources, Apr 2022]

C11orf80 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6

Variant 11-66756337-CT-C is Benign according to our data. Variant chr11-66756337-CT-C is described in ClinVar as [Likely_benign]. Clinvar id is 3055765.Status of the report is no_assertion_criteria_provided, 0 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0111 (1659/149214) while in subpopulation NFE AF= 0.0159 (1066/67076). AF 95% confidence interval is 0.0151. There are 12 homozygotes in gnomad4. There are 760 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 12 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C11orf80	NM_001302084.2 linkuse as main transcript	c.-29-2696del		intron_variant		ENST00000540737.7	NP_001289013.1
C11orf80	NM_024650.3 linkuse as main transcript	c.317-6del		splice_polypyrimidine_tract_variant, intron_variant			NP_078926.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C11orf80	ENST00000540737.7 linkuse as main transcript	c.-29-2696del		intron_variant		2	NM_001302084.2	ENSP00000444319	A2

Frequencies

GnomAD3 genomes

AF:

0.0111

AC:

1659

AN:

149118

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00546

Gnomad AMI

AF:

0.0298

Gnomad AMR

AF:

0.0153

Gnomad ASJ

AF:

0.0134

Gnomad EAS

AF:

0.000391

Gnomad SAS

AF:

0.00470

Gnomad FIN

AF:

0.00130

Gnomad MID

AF:

0.0128

Gnomad NFE

AF:

0.0159

Gnomad OTH

AF:

0.0148

GnomAD3 exomes

AF:

0.0411

AC:

1044

AN:

25382

Hom.:

AF XY:

0.0407

AC XY:

566

AN XY:

13902

show subpopulations

Gnomad AFR exome

AF:

0.0300

Gnomad AMR exome

AF:

0.0426

Gnomad ASJ exome

AF:

0.0536

Gnomad EAS exome

AF:

0.0153

Gnomad SAS exome

AF:

0.0332

Gnomad FIN exome

AF:

0.0309

Gnomad NFE exome

AF:

0.0483

Gnomad OTH exome

AF:

0.0430

GnomAD4 exome

AF:

0.0158

AC:

14737

AN:

932494

Hom.:

Cov.:

AF XY:

0.0158

AC XY:

7123

AN XY:

450934

show subpopulations

Gnomad4 AFR exome

AF:

0.00721

Gnomad4 AMR exome

AF:

0.0198

Gnomad4 ASJ exome

AF:

0.0197

Gnomad4 EAS exome

AF:

0.00538

Gnomad4 SAS exome

AF:

0.00995

Gnomad4 FIN exome

AF:

0.00878

Gnomad4 NFE exome

AF:

0.0164

Gnomad4 OTH exome

AF:

0.0163

GnomAD4 genome

AF:

0.0111

AC:

1659

AN:

149214

Hom.:

Cov.:

AF XY:

0.0104

AC XY:

760

AN XY:

72734

show subpopulations

Gnomad4 AFR

AF:

0.00544

Gnomad4 AMR

AF:

0.0153

Gnomad4 ASJ

AF:

0.0134

Gnomad4 EAS

AF:

0.000392

Gnomad4 SAS

AF:

0.00470

Gnomad4 FIN

AF:

0.00130

Gnomad4 NFE

AF:

0.0159

Gnomad4 OTH

AF:

0.0147

Bravo

AF:

0.0125

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

TOP6BL-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 22, 2019

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over